I recommend RevoUninstaller.com
It will execute the normal uninstall routine + scan for left-over registry entries, files and folders.
Another solution might be this:
"You may need to manually remove the game folder, and delete 2 Registry Keys before you'll be able to re-install.
Go to C:\Program Files\Stardock Games\Sins of a Solar Empire (or where ever you installed the game) and delete the main folder.
Then launch the System Registry (Start-> run, and type regedit)
Look for and delete the following Keys;
HKEY_LOCAL_MACHINE\SOFTWARE\Stardock\Drengin.net\sins
HKEY_LOCAL_MACHINE\SOFTWARE\Stardock\Drengin.net\sinsentrench
For Vista 64 bit;
HKLM>SOFTWARE>Wow6432Node>Stardock>Drengin.net>sins
HKLM>SOFTWARE>Wow6432Node>Stardock>Drengin.net>sinsentrench
Then, reboot your PC and go back to Impulse and try installing the base game. Make sure it installs to 1.13 version, test it out before then installing entrenchment."
If that doesn't work either, you schould write to [email protected].